MOTIVATION: Large-scale detection and classification of alternative splicing and transcriptional initiation (ASTI) is the first step towards detailed studies of the functional implication and mechanisms of these phenomena. RESULTS: We have developed an algorithm that classifies all observed units of ASTI into an extendable set of distinct types (e.g. cassette type) by converting a collection of alignments between a genomic DNA sequence and cDNA sequences into binary description. This description system can uniquely and compactly encode not only typical patterns but also any rare patterns that are usually collectively assigned to 'others.' More than 150 distinct ASTI types were found when this system was applied to genome-wide detection of ASTI units in human and five other eukaryotes. AVAILABILITY: The data detected by this system are available through ASTRA (http://alterna.cbrc.jp/), a database equipped with a Java-based browser that can interactively reorganize the order of displayed splicing patterns on demand.
MOTIVATION: Large-scale detection and classification of alternative splicing and transcriptional initiation (ASTI) is the first step towards detailed studies of the functional implication and mechanisms of these phenomena. RESULTS: We have developed an algorithm that classifies all observed units of ASTI into an extendable set of distinct types (e.g. cassette type) by converting a collection of alignments between a genomic DNA sequence and cDNA sequences into binary description. This description system can uniquely and compactly encode not only typical patterns but also any rare patterns that are usually collectively assigned to 'others.' More than 150 distinct ASTI types were found when this system was applied to genome-wide detection of ASTI units in human and five other eukaryotes. AVAILABILITY: The data detected by this system are available through ASTRA (http://alterna.cbrc.jp/), a database equipped with a Java-based browser that can interactively reorganize the order of displayed splicing patterns on demand.
Authors: José Eduardo Kroll; Pedro A F Galante; Daniel T Ohara; Fábio C P Navarro; Lucila Ohno-Machado; Sandro J de Souza Journal: RNA Biol Date: 2012-10-12 Impact factor: 4.652
Authors: Roxana S Redis; Luz E Vela; Weiqin Lu; Juliana Ferreira de Oliveira; Cristina Ivan; Cristian Rodriguez-Aguayo; Douglas Adamoski; Barbara Pasculli; Ayumu Taguchi; Yunyun Chen; Agustin F Fernandez; Luis Valledor; Katrien Van Roosbroeck; Samuel Chang; Maitri Shah; Garrett Kinnebrew; Leng Han; Yaser Atlasi; Lawrence H Cheung; Gilbert Y Huang; Paloma Monroig; Marc S Ramirez; Tina Catela Ivkovic; Long Van; Hui Ling; Roberta Gafà; Sanja Kapitanovic; Giovanni Lanza; James A Bankson; Peng Huang; Stephen Y Lai; Robert C Bast; Michael G Rosenblum; Milan Radovich; Mircea Ivan; Geoffrey Bartholomeusz; Han Liang; Mario F Fraga; William R Widger; Samir Hanash; Ioana Berindan-Neagoe; Gabriel Lopez-Berestein; Andre L B Ambrosio; Sandra M Gomes Dias; George A Calin Journal: Mol Cell Date: 2016-02-04 Impact factor: 17.970
Authors: Alissa M Resch; Aleksey Y Ogurtsov; Igor B Rogozin; Svetlana A Shabalina; Eugene V Koonin Journal: BMC Genomics Date: 2009-04-16 Impact factor: 3.969